Our group is mainly involved in microbial genomics and epigenomics research topics:

Toxin-antitoxin systems

We are part of a Sinergia project dedicated to the identification and analysis of toxin-antitoxin systems in relationship to the antibiotic resistance phenotypes. The subject has been recognized of critical importance by the World Health Organization (WHO) in its global action plan to combat antimicrobial resistance. We use Next Generation Sequencing (NGS) experiments (e.g. Tn-seq, Mut-seq, Shotgun-seq and nEMOTE-seq) to identify toxin-antitoxin genes and their targets.

DNA methylations in prokaryotes

As a secondary topic, we are interested in extracting DNA methylation information from PacBio sequencing data to compare DNA methylations in prokaryotes. We developed a tool called PACMAN to visualize graphically methylated motifs in bacterial genomes.

Other research topics covered as part of the core facility services:

  • genome assembly
  • annotation and comparative genomics using next generation sequencing (NGS) data
  • transcriptomics analysis using NGS data
  • metagenomics
  • mutant and structure variant identification by resequencing
  • ChIPseq data analysis
  • proteome clustering and ortholog/paralog classification
  • pathway and gene set enrichment analysis

More information about our research and our core facility